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- PDB-7brn: Crystal structure of Atg40 AIM fused to Atg8 -

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Basic information

Entry
Database: PDB / ID: 7brn
TitleCrystal structure of Atg40 AIM fused to Atg8
ComponentsAutophagy-related protein 40,Autophagy-related protein 8
KeywordsMEMBRANE PROTEIN / autophagy / endoplasmic reticulum
Function / homology
Function and homology information


Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / lipid droplet formation / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cortical endoplasmic reticulum / cytoplasm to vacuole targeting by the Cvt pathway ...Cvt vesicle membrane / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / lipid droplet formation / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cortical endoplasmic reticulum / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein-containing complex localization / phosphatidylethanolamine binding / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / cellular response to nitrogen starvation / autophagy of mitochondrion / autophagosome membrane / autophagosome maturation / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of macroautophagy / autophagosome / lipid droplet / mitochondrial membrane / autophagy / protein tag activity / protein-macromolecule adaptor activity / membrane fusion / endoplasmic reticulum membrane / membrane / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
L-EPINEPHRINE / Autophagy-related protein 8 / Autophagy-related protein 40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.231 Å
AuthorsYamasaki, A. / Noda, N.N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K18339 Japan
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Science and TechnologyJPMJCR13M7 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes.
Authors: Mochida, K. / Yamasaki, A. / Matoba, K. / Kirisako, H. / Noda, N.N. / Nakatogawa, H.
History
DepositionMar 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein 40,Autophagy-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8964
Polymers15,5891
Non-polymers3073
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-1 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.729, 74.729, 57.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Autophagy-related protein 40,Autophagy-related protein 8


Mass: 15588.764 Da / Num. of mol.: 1 / Mutation: K26P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Gene: ATG40, YOR152C, O3536, ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99325, UniProt: P38182
#2: Chemical ChemComp-ALE / L-EPINEPHRINE / ADRENALINE


Mass: 183.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO3 / Comment: medication, hormone*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 8000, 0.1M HEPES pH 7.5, 8% Ethylene glycol, 0.04% Cortisone, 0.04% Epinephrine, 0.04% Protoporphyrin disodium salt, 0.04% Pyridoxine, 0.04% Thymidine monophosphate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.231→42.813 Å / Num. obs: 9229 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 36.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.04754 / Rrim(I) all: 0.1486 / Net I/σ(I): 13.78
Reflection shellResolution: 2.231→2.311 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.5954 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 900 / CC1/2: 0.953 / CC star: 0.988 / Rpim(I) all: 0.2354 / Rrim(I) all: 0.6415 / % possible all: 97.91

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
XDSdata reduction
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZPN

2zpn


Resolution: 2.231→42.813 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 462 5.01 %
Rwork0.203 8767 -
obs0.2039 9229 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.18 Å2 / Biso mean: 46.5041 Å2 / Biso min: 19.22 Å2
Refinement stepCycle: final / Resolution: 2.231→42.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 46 42 1164
Biso mean--60.14 44.72 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2314-2.55430.31591500.2632285699
2.5543-3.2180.23571530.22062900100
3.218-42.8130.19321590.18263011100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.64620.11581.8223.5438-1.36896.50150.0826-0.6527-0.0585-0.24230.3002-0.0095-0.30420.1137-0.38570.3598-0.01880.03350.40930.02180.2261-34.1568-22.873411.8344
27.11670.6651-1.85588.63094.51693.0325-0.0036-0.29360.2905-0.9809-0.5014-0.8139-0.59911.62430.39640.61930.0398-0.00870.82310.11160.6539-19.0548-28.636611.9045
35.5404-2.78314.39974.0763-3.89195.3879-0.07020.513-0.0875-0.0487-0.1527-0.23570.09830.69990.18280.31380.03530.02840.3971-0.06390.2467-26.6427-22.4084-11.5748
44.4761-0.38324.41183.77891.10624.9172-0.62370.13170.33280.14890.0136-0.1636-0.90470.28560.62330.4149-0.0557-0.02710.30580.01380.2554-29.8847-12.3824-8.1708
54.1872-0.4253-1.05345.77382.161.1673-0.1511-0.3020.0020.0190.086-0.3108-0.39570.12390.13260.3924-0.0624-0.0140.33950.00740.2537-29.0313-13.04050.6664
63.88680.64-0.74453.4449-1.81976.21450.1121-0.30470.40010.7312-0.1391-0.045-0.76130.59290.03690.7671-0.1039-0.07140.3258-0.0270.3673-26.6397-5.59384.0189
76.67720.53212.40522.60212.91764.0143-0.00090.03820.3801-0.2948-0.1961-0.3417-0.80730.94940.12690.4554-0.13460.0560.57170.03150.3183-21.2898-9.9994-11.7507
83.8036-1.77351.32612.4912-0.51490.54740.1206-1.18340.10060.9967-0.0348-0.4959-0.60890.9943-0.21330.7202-0.1374-0.15010.7084-0.05320.3002-21.4996-12.70425.5804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 19 )A12 - 19
3X-RAY DIFFRACTION3chain 'A' and (resid 20 through 42 )A20 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 53 )A43 - 53
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 74 )A54 - 74
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 108 )A75 - 108
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 122 )A109 - 122
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 133 )A123 - 133

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